› 2xcr

X-ray diffraction
3.5Å resolution

The 3.5A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus DNA Gyrase complexed with GSK299423 and DNA

Released:
DOI: 10.2210/pdb2xcr/pdb
PDB entry 2xcr coloured by chain, front view.
PDB entry 2xcr coloured by chain, side view.
PDB entry 2xcr coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus N315
Primary publication:
Type IIA topoisomerase inhibition by a new class of antibacterial agents.
Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR, Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders MR, Singh O, Spitzfaden CE, Shen C, Shillings A, Theobald AJ, Wohlkonig A, Pearson ND, Gwynn MN
Nature 466 935-40 (2010)
PMID: 20686482

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218928 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA gyrase subunit A; DNA gyrase subunit B Chains: B, D, S, U
Molecule details ›
Chains: B, D, S, U
Length: 726 amino acids
Theoretical weight: 82.33 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P66937 (Residues: 410-644; Coverage: 37%)
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0005, SA0006, gyrA, gyrB
Sequence domains:
Structure domains:
5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3' Chains: E, F
Molecule details ›
Chains: E, F
Length: 20 nucleotides
Theoretical weight: 6.1 KDa
5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3' Chains: V, W
Molecule details ›
Chains: V, W
Length: 20 nucleotides
Theoretical weight: 6.14 KDa

Ligands and Environments

1 bound ligand:
Ligand RXV 2 x RXV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 113.26Å b: 165.381Å c: 308.431Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.258
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

57 review citations

Drugging topoisomerases: lessons and challenges.
Pommier Y. (2013)
56 more

6 mentions without citation

Interfacial inhibitors.
Pommier et al. (2015)
5 more